Taxonomy_MILK

16S sequencing data - cow milk samples

## `summarise()` has grouped output by 'timepoint', 'treatment'. You can override using the `.groups` argument.

## # A tibble: 16 × 6
## # Groups:   treatment [2]
##    treatment Cow_ID     `0`   `8`  `21`  `28`
##    <chr>     <chr>    <int> <int> <int> <int>
##  1 Control   4251 AG      1     1     1     1
##  2 Control   4251 ARD     1     1     1     1
##  3 Control   4330 ARD     1     1     1     1
##  4 Control   5303 ARD     1     1     1     1
##  5 Control   6201 AG      1     1     1     1
##  6 Control   6201 ARG     1     1     1     1
##  7 Control   6221 ARG     1     1     1     1
##  8 Control   6249 AG      1     1     1     1
##  9 Treated   4252 AD      1     1     1     1
## 10 Treated   4252 AG      1     1     1     1
## 11 Treated   4287 AG      1     1     1     1
## 12 Treated   5240 AD      1     1     1     1
## 13 Treated   5240 ARD     1     1     1     1
## 14 Treated   5250 AD      1     1     1     1
## 15 Treated   6261 ARD     1     1     1     1
## 16 Treated   7249 ARG     1     1     1     1

Treatments and timepoints

First, let’s look at phyla:

phylum	treatment	timepoint	N	avg_abund	std
Firmicutes	Control	28	8	0.2414	0.119
Firmicutes	Control	21	8	0.2753	0.090
Firmicutes	Control	8	8	0.3945	0.129
Firmicutes	Control	0	8	0.4610	0.127
Proteobacteria	Control	0	8	0.2176	0.104
Proteobacteria	Control	8	8	0.2911	0.147
Proteobacteria	Control	21	8	0.3559	0.111
Proteobacteria	Control	28	8	0.4594	0.161
Actinobacteria	Control	0	8	0.1225	0.059
Actinobacteria	Control	8	8	0.1344	0.049
Actinobacteria	Control	21	8	0.1785	0.029
Actinobacteria	Control	28	8	0.1785	0.045
Bacteroidetes	Control	28	8	0.0766	0.050
Bacteroidetes	Control	21	8	0.1120	0.035
Bacteroidetes	Control	8	8	0.1148	0.026
Bacteroidetes	Control	0	8	0.1341	0.023
Firmicutes	Treated	28	8	0.3689	0.108
Firmicutes	Treated	8	8	0.3781	0.123
Firmicutes	Treated	21	8	0.4007	0.147
Firmicutes	Treated	0	8	0.4081	0.087
Proteobacteria	Treated	21	8	0.2458	0.127
Proteobacteria	Treated	0	8	0.2507	0.079
Proteobacteria	Treated	8	8	0.2855	0.147
Proteobacteria	Treated	28	8	0.3000	0.164
Actinobacteria	Treated	21	8	0.1149	0.038
Actinobacteria	Treated	0	8	0.1438	0.033
Actinobacteria	Treated	28	8	0.1540	0.021
Actinobacteria	Treated	8	8	0.1577	0.039
Bacteroidetes	Treated	28	8	0.1135	0.044
Bacteroidetes	Treated	8	8	0.1147	0.035
Bacteroidetes	Treated	0	8	0.1308	0.021
Bacteroidetes	Treated	21	8	0.1487	0.025

###boxplot abundances per timepoint and treatment

##Phyla

Treatments, all taxonomic levels

## 
##     2     3     4     5     6 
##  2048  4416 10496 24832 69120

A table of relative abundances (and standard deviations) per taxa and treatment:

level	new_taxa	treatment	timepoint	avg_abund	std
class	Clostridia	Control	0	0.3587	0.158
class	Gammaproteobacteria	Control	28	0.3224	0.102
class	Clostridia	Treated	21	0.2907	0.161
class	Clostridia	Treated	0	0.2875	0.092
class	Clostridia	Control	8	0.2556	0.132
class	Clostridia	Treated	28	0.2478	0.086
class	Clostridia	Treated	8	0.2419	0.118
class	Gammaproteobacteria	Control	21	0.2209	0.068
class	Gammaproteobacteria	Treated	28	0.2116	0.113
class	Gammaproteobacteria	Control	8	0.1972	0.100
class	Gammaproteobacteria	Treated	0	0.1826	0.042
class	Gammaproteobacteria	Treated	8	0.1801	0.098
class	Clostridia	Control	21	0.1766	0.084
class	Actinobacteria	Control	28	0.1734	0.048
class	Gammaproteobacteria	Treated	21	0.1602	0.092
class	Actinobacteria	Control	21	0.1590	0.031
class	Gammaproteobacteria	Control	0	0.1545	0.067
class	Bacteroidia	Treated	21	0.1487	0.025
class	Actinobacteria	Treated	8	0.1444	0.037
class	Clostridia	Control	28	0.1438	0.102
class	Actinobacteria	Treated	28	0.1416	0.019
class	Alphaproteobacteria	Control	28	0.1358	0.068
class	Bacteroidia	Control	0	0.1341	0.023
class	Actinobacteria	Treated	0	0.1334	0.031
class	Alphaproteobacteria	Control	21	0.1331	0.050
class	Bacteroidia	Treated	0	0.1308	0.021
class	Bacilli	Control	8	0.1244	0.054
class	Actinobacteria	Control	8	0.1237	0.047
class	Bacilli	Treated	8	0.1227	0.032
class	Bacteroidia	Control	8	0.1148	0.026
class	Bacteroidia	Treated	8	0.1147	0.035
class	Bacteroidia	Treated	28	0.1135	0.044
class	Bacteroidia	Control	21	0.1120	0.035
class	Actinobacteria	Control	0	0.1109	0.060
class	Bacilli	Treated	28	0.1079	0.022
class	Bacilli	Treated	0	0.1061	0.013
class	Actinobacteria	Treated	21	0.1008	0.038
class	Alphaproteobacteria	Treated	8	0.0995	0.051
class	Bacilli	Treated	21	0.0952	0.036
class	Alphaproteobacteria	Control	8	0.0915	0.050
class	Bacilli	Control	21	0.0877	0.022
class	Bacilli	Control	0	0.0864	0.044
class	Alphaproteobacteria	Treated	28	0.0857	0.057
class	Bacilli	Control	28	0.0856	0.029
class	Alphaproteobacteria	Treated	21	0.0810	0.043
class	Bacteroidia	Control	28	0.0766	0.050
class	Alphaproteobacteria	Treated	0	0.0649	0.044
class	Alphaproteobacteria	Control	0	0.0599	0.042
class	Erysipelotrichia	Control	8	0.0104	0.004
family	Ruminococcaceae	Control	0	0.2013	0.119
family	Ruminococcaceae	Treated	21	0.1613	0.110
family	Pseudomonadaceae	Control	28	0.1409	0.065
family	Ruminococcaceae	Treated	0	0.1397	0.057
family	Ruminococcaceae	Control	8	0.1210	0.088
family	Ruminococcaceae	Treated	8	0.1189	0.067
family	Ruminococcaceae	Treated	28	0.1167	0.041
family	Pseudomonadaceae	Control	21	0.0825	0.045
family	Ruminococcaceae	Control	21	0.0813	0.051
family	Propionibacteriaceae	Control	28	0.0759	0.028
family	Ruminococcaceae	Control	28	0.0757	0.054
family	Lachnospiraceae	Control	0	0.0734	0.018
family	Beijerinckiaceae	Control	28	0.0675	0.032
family	Pseudomonadaceae	Treated	28	0.0672	0.071
family	Pseudomonadaceae	Control	8	0.0668	0.061
family	Lachnospiraceae	Treated	0	0.0626	0.023
family	Lachnospiraceae	Control	8	0.0598	0.019
family	Pseudomonadaceae	Treated	8	0.0593	0.055
family	Lachnospiraceae	Treated	21	0.0590	0.030
family	Lachnospiraceae	Treated	28	0.0582	0.023
family	Lachnospiraceae	Treated	8	0.0558	0.021
family	Moraxellaceae	Control	28	0.0522	0.012
family	Halomonadaceae	Control	28	0.0514	0.021
family	Pseudomonadaceae	Treated	0	0.0507	0.027
family	Pseudomonadaceae	Treated	21	0.0497	0.042
family	Beijerinckiaceae	Control	8	0.0459	0.037
family	Moraxellaceae	Treated	28	0.0456	0.010
family	Pseudomonadaceae	Control	0	0.0454	0.029
family	Beijerinckiaceae	Control	21	0.0453	0.022
family	Propionibacteriaceae	Treated	28	0.0445	0.021
family	Moraxellaceae	Treated	0	0.0441	0.011
family	Staphylococcaceae	Control	8	0.0438	0.048
family	Prevotellaceae	Treated	21	0.0427	0.018
family	Beijerinckiaceae	Treated	8	0.0424	0.029
family	Lachnospiraceae	Control	21	0.0423	0.015
family	Staphylococcaceae	Treated	8	0.0411	0.016
family	Moraxellaceae	Control	8	0.0405	0.014
family	Propionibacteriaceae	Control	21	0.0396	0.021
family	Propionibacteriaceae	Treated	0	0.0389	0.014
family	Propionibacteriaceae	Control	0	0.0379	0.026
family	Propionibacteriaceae	Control	8	0.0379	0.021
family	Prevotellaceae	Treated	0	0.0371	0.008
family	Moraxellaceae	Control	0	0.0369	0.020
family	Prevotellaceae	Control	8	0.0364	0.009
family	Moraxellaceae	Treated	8	0.0363	0.019
family	Propionibacteriaceae	Treated	8	0.0359	0.019
family	Prevotellaceae	Control	0	0.0354	0.007
family	Micrococcaceae	Treated	28	0.0352	0.014
family	Micrococcaceae	Control	28	0.0348	0.016
family	Micrococcaceae	Treated	0	0.0348	0.009
family	Beijerinckiaceae	Treated	28	0.0345	0.030
family	Rikenellaceae	Control	0	0.0345	0.014
family	Moraxellaceae	Control	21	0.0344	0.013
family	Micrococcaceae	Treated	8	0.0338	0.012
family	Prevotellaceae	Treated	28	0.0333	0.012
family	Halomonadaceae	Control	21	0.0329	0.015
family	Rikenellaceae	Treated	0	0.0329	0.013
family	Halomonadaceae	Control	8	0.0324	0.024
family	Prevotellaceae	Treated	8	0.0322	0.011
family	Rikenellaceae	Treated	21	0.0322	0.017
family	Lachnospiraceae	Control	28	0.0317	0.026
family	Staphylococcaceae	Control	28	0.0316	0.022
family	Christensenellaceae	Control	0	0.0312	0.025
family	Rikenellaceae	Treated	28	0.0311	0.014
family	Halomonadaceae	Treated	28	0.0303	0.021
family	Streptococcaceae	Control	8	0.0299	0.013
family	Streptococcaceae	Treated	28	0.0296	0.015
family	Streptococcaceae	Treated	0	0.0290	0.011
family	Micrococcaceae	Control	0	0.0287	0.018
family	Micrococcaceae	Control	8	0.0287	0.011
family	Moraxellaceae	Treated	21	0.0275	0.018
family	Staphylococcaceae	Treated	28	0.0273	0.013
family	Prevotellaceae	Control	28	0.0272	0.021
family	Rhizobiaceae	Control	28	0.0268	0.023
family	Christensenellaceae	Treated	0	0.0261	0.011
family	Staphylococcaceae	Control	21	0.0261	0.015
family	Prevotellaceae	Control	21	0.0260	0.010
family	Halomonadaceae	Treated	8	0.0258	0.019
family	Rikenellaceae	Control	8	0.0256	0.009
family	Streptococcaceae	Control	0	0.0256	0.017
family	Sphingomonadaceae	Control	21	0.0253	0.012
family	Beijerinckiaceae	Treated	21	0.0252	0.021
family	Rhizobiaceae	Control	21	0.0248	0.018
family	Rikenellaceae	Treated	8	0.0247	0.014
family	Beijerinckiaceae	Treated	0	0.0246	0.018
family	Streptococcaceae	Treated	8	0.0244	0.012
family	Christensenellaceae	Treated	21	0.0242	0.015
family	Corynebacteriaceae	Control	21	0.0239	0.014
family	Micrococcaceae	Control	21	0.0239	0.008
family	Beijerinckiaceae	Control	0	0.0236	0.017
family	Micrococcaceae	Treated	21	0.0235	0.018
family	Propionibacteriaceae	Treated	21	0.0234	0.016
family	Burkholderiaceae	Control	21	0.0230	0.011
family	Christensenellaceae	Control	8	0.0229	0.021
family	Staphylococcaceae	Treated	21	0.0228	0.012
family	Halomonadaceae	Treated	0	0.0226	0.007
family	Streptococcaceae	Treated	21	0.0226	0.018
family	Staphylococcaceae	Treated	0	0.0224	0.009
family	Halomonadaceae	Control	0	0.0217	0.010
family	Halomonadaceae	Treated	21	0.0216	0.015
family	Corynebacteriaceae	Treated	8	0.0214	0.009
family	Corynebacteriaceae	Control	8	0.0207	0.015
family	Staphylococcaceae	Control	0	0.0207	0.011
family	Bacteroidaceae	Control	0	0.0205	0.009
family	Peptostreptococcaceae	Treated	28	0.0204	0.005
family	Christensenellaceae	Treated	28	0.0202	0.008
family	Corynebacteriaceae	Control	28	0.0201	0.010
family	Peptostreptococcaceae	Treated	8	0.0197	0.007
family	Corynebacteriaceae	Treated	0	0.0194	0.005
family	Corynebacteriaceae	Treated	28	0.0190	0.007
family	Rikenellaceae	Control	28	0.0188	0.013
family	Peptostreptococcaceae	Treated	0	0.0187	0.004
family	Sphingomonadaceae	Treated	8	0.0182	0.013
family	Streptococcaceae	Control	28	0.0181	0.014
family	Carnobacteriaceae	Treated	0	0.0178	0.007
family	Rhizobiaceae	Treated	28	0.0174	0.016
family	Rikenellaceae	Control	21	0.0173	0.009
family	Peptostreptococcaceae	Control	21	0.0168	0.011
family	Christensenellaceae	Treated	8	0.0166	0.013
family	Bacteroidaceae	Treated	21	0.0165	0.010
family	Burkholderiaceae	Control	28	0.0165	0.009
family	Bacteroidaceae	Treated	0	0.0164	0.006
family	Streptococcaceae	Control	21	0.0161	0.010
family	Bacillaceae	Treated	8	0.0159	0.008
family	Peptostreptococcaceae	Control	8	0.0159	0.009
family	Flavobacteriaceae	Control	21	0.0156	0.011
family	Nocardioidaceae	Control	21	0.0154	0.010
family	Sphingomonadaceae	Treated	21	0.0154	0.016
family	Corynebacteriaceae	Control	0	0.0153	0.010
family	Rhizobiaceae	Treated	21	0.0152	0.009
family	Bacillaceae	Control	21	0.0151	0.010
family	Peptostreptococcaceae	Control	0	0.0146	0.007
family	Peptostreptococcaceae	Treated	21	0.0136	0.005
family	Carnobacteriaceae	Treated	8	0.0135	0.007
family	Bacillaceae	Treated	21	0.0132	0.006
family	Carnobacteriaceae	Control	0	0.0132	0.008
family	Carnobacteriaceae	Treated	21	0.0132	0.007
family	Carnobacteriaceae	Treated	28	0.0132	0.006
family	Carnobacteriaceae	Control	8	0.0131	0.008
family	Bacteroidaceae	Control	8	0.0130	0.014
family	Family XIII	Control	0	0.0130	0.008
family	Flavobacteriaceae	Treated	21	0.0129	0.013
family	Microbacteriaceae	Control	21	0.0124	0.008
family	Bacteroidaceae	Treated	8	0.0121	0.005
family	Sphingomonadaceae	Control	8	0.0121	0.006
family	Sphingomonadaceae	Control	28	0.0121	0.009
family	Lactobacillaceae	Treated	28	0.0120	0.008
family	Clostridiaceae 1	Treated	0	0.0119	0.007
family	Shewanellaceae	Control	28	0.0119	0.006
family	Burkholderiaceae	Control	8	0.0118	0.011
family	Burkholderiaceae	Treated	21	0.0118	0.008
family	Sphingomonadaceae	Treated	0	0.0118	0.014
family	Xanthobacteraceae	Control	21	0.0118	0.005
family	Burkholderiaceae	Treated	8	0.0117	0.006
family	Christensenellaceae	Control	21	0.0117	0.011
family	Xanthomonadaceae	Control	21	0.0117	0.005
family	Rhizobiaceae	Treated	8	0.0110	0.005
family	Flavobacteriaceae	Treated	0	0.0109	0.002
family	Family XIII	Treated	0	0.0108	0.004
family	Bacteroidaceae	Treated	28	0.0106	0.007
family	Corynebacteriaceae	Treated	21	0.0106	0.006
family	Rhizobiaceae	Control	0	0.0105	0.008
family	Bacillaceae	Control	8	0.0104	0.008
family	Erysipelotrichaceae	Control	8	0.0104	0.004
family	Clostridiaceae 1	Control	8	0.0103	0.006
genus	Pseudomonas	Control	28	0.1405	0.065
genus	Pseudomonas	Control	21	0.0825	0.045
genus	Cutibacterium	Control	28	0.0734	0.028
genus	Pseudomonas	Treated	28	0.0671	0.071
genus	Pseudomonas	Control	8	0.0666	0.061
genus	Methylobacterium	Control	28	0.0603	0.033
genus	Pseudomonas	Treated	8	0.0592	0.055
genus	Halomonas	Control	28	0.0511	0.021
genus	Pseudomonas	Treated	0	0.0504	0.028
genus	Pseudomonas	Treated	21	0.0495	0.043
genus	Ruminococcaceae UCG-010	Control	0	0.0459	0.025
genus	Pseudomonas	Control	0	0.0453	0.029
genus	Cutibacterium	Treated	28	0.0416	0.021
genus	Methylobacterium	Control	21	0.0401	0.022
genus	Methylobacterium	Control	8	0.0394	0.035
genus	Ruminococcaceae UCG-005	Control	0	0.0393	0.020
genus	Staphylococcus	Control	8	0.0384	0.047
genus	Staphylococcus	Treated	8	0.0367	0.017
genus	Cutibacterium	Control	0	0.0365	0.027
genus	Ruminococcaceae UCG-010	Treated	21	0.0362	0.023
genus	Cutibacterium	Control	21	0.0361	0.022
genus	Cutibacterium	Treated	0	0.0360	0.014
genus	Ruminococcaceae UCG-005	Treated	21	0.0356	0.026
genus	Ruminococcaceae UCG-010	Treated	0	0.0354	0.015
genus	Cutibacterium	Control	8	0.0350	0.022
genus	Methylobacterium	Treated	8	0.0349	0.027
genus	Halomonas	Control	21	0.0320	0.015
genus	Halomonas	Control	8	0.0313	0.024
genus	Christensenellaceae R-7 group	Control	0	0.0308	0.025
genus	Cutibacterium	Treated	8	0.0307	0.019
genus	Ruminococcaceae UCG-005	Treated	0	0.0303	0.015
genus	Halomonas	Treated	28	0.0298	0.022
genus	Streptococcus	Control	8	0.0298	0.013
genus	Ruminococcaceae UCG-010	Control	8	0.0295	0.018
genus	Psychrobacter	Treated	0	0.0292	0.010
genus	Ruminococcaceae UCG-010	Treated	28	0.0291	0.013
genus	Streptococcus	Treated	28	0.0287	0.015
genus	Ruminococcaceae UCG-005	Control	8	0.0286	0.026
genus	Psychrobacter	Treated	28	0.0283	0.007
genus	Streptococcus	Treated	0	0.0283	0.010
genus	Ruminococcaceae UCG-010	Treated	8	0.0277	0.020
genus	Methylobacterium	Treated	28	0.0276	0.029
genus	Staphylococcus	Control	28	0.0272	0.020
genus	Psychrobacter	Control	8	0.0271	0.008
genus	Christensenellaceae R-7 group	Treated	0	0.0259	0.011
genus	Streptococcus	Control	0	0.0254	0.017
genus	Halomonas	Treated	8	0.0251	0.019
genus	Psychrobacter	Control	0	0.0249	0.014
genus	Ruminococcaceae UCG-005	Treated	8	0.0244	0.013
genus	Staphylococcus	Treated	28	0.0243	0.012
genus	Christensenellaceae R-7 group	Treated	21	0.0241	0.015
genus	Ruminococcaceae UCG-005	Treated	28	0.0241	0.007
genus	Psychrobacter	Control	28	0.0233	0.013
genus	Streptococcus	Treated	8	0.0233	0.011
genus	Psychrobacter	Treated	8	0.0232	0.008
genus	Christensenellaceae R-7 group	Control	8	0.0227	0.021
genus	Staphylococcus	Control	21	0.0224	0.017
genus	Rikenellaceae RC9 gut group	Treated	28	0.0223	0.010
genus	Acinetobacter	Control	28	0.0221	0.011
genus	[Eubacterium] coprostanoligenes group	Control	0	0.0219	0.009
genus	Halomonas	Treated	0	0.0219	0.008
genus	Methylobacterium	Treated	21	0.0219	0.022
genus	Rikenellaceae RC9 gut group	Treated	21	0.0219	0.011
genus	Ruminococcaceae UCG-013	Control	0	0.0218	0.021
genus	Prevotella 1	Treated	21	0.0217	0.011
genus	Streptococcus	Treated	21	0.0217	0.018
genus	Rikenellaceae RC9 gut group	Control	0	0.0213	0.008
genus	Halomonas	Treated	21	0.0212	0.015
genus	Halomonas	Control	0	0.0211	0.010
genus	Cutibacterium	Treated	21	0.0209	0.015
genus	Rikenellaceae RC9 gut group	Treated	0	0.0207	0.009
genus	Bacteroides	Control	0	0.0205	0.009
genus	Psychrobacter	Treated	21	0.0203	0.016
genus	Christensenellaceae R-7 group	Treated	28	0.0202	0.008
genus	Prevotella 1	Control	28	0.0197	0.017
genus	Prevotella 1	Control	8	0.0196	0.008
genus	Methylobacterium	Treated	0	0.0194	0.019
genus	Staphylococcus	Treated	21	0.0194	0.013
genus	[Eubacterium] coprostanoligenes group	Treated	21	0.0192	0.011
genus	[Eubacterium] coprostanoligenes group	Treated	0	0.0190	0.009
genus	Staphylococcus	Treated	0	0.0190	0.006
genus	Staphylococcus	Control	0	0.0189	0.011
genus	Ruminococcaceae UCG-005	Control	21	0.0187	0.011
genus	[Eubacterium] coprostanoligenes group	Treated	28	0.0185	0.009
genus	Methylobacterium	Control	0	0.0184	0.014
genus	Psychrobacter	Control	21	0.0183	0.009
genus	Ruminococcaceae UCG-010	Control	28	0.0177	0.016
genus	Ruminococcaceae UCG-005	Control	28	0.0176	0.018
genus	Streptococcus	Control	28	0.0176	0.013
genus	Rikenellaceae RC9 gut group	Control	8	0.0174	0.007
genus	[Eubacterium] coprostanoligenes group	Treated	8	0.0169	0.008
genus	Ruminococcaceae UCG-010	Control	21	0.0169	0.018
genus	Christensenellaceae R-7 group	Treated	8	0.0166	0.013
genus	Bacteroides	Treated	21	0.0165	0.010
genus	Bacteroides	Treated	0	0.0164	0.006
genus	Prevotella 1	Treated	8	0.0164	0.007
genus	Corynebacterium 1	Control	21	0.0163	0.010
genus	Corynebacterium 1	Treated	8	0.0161	0.007
genus	Prevotella 1	Control	21	0.0161	0.009
genus	Ruminococcaceae UCG-013	Treated	21	0.0161	0.015
genus	Prevotella 1	Treated	0	0.0157	0.008
genus	Streptococcus	Control	21	0.0157	0.010
genus	Corynebacterium 1	Control	8	0.0154	0.012
genus	Rikenellaceae RC9 gut group	Treated	8	0.0148	0.008
genus	Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium	Control	28	0.0144	0.014
genus	Prevotella 1	Control	0	0.0143	0.006
genus	Prevotella 1	Treated	28	0.0140	0.004
genus	Corynebacterium 1	Treated	0	0.0139	0.003
genus	Ruminococcaceae UCG-014	Control	0	0.0138	0.012
genus	Lachnospiraceae NK3A20 group	Treated	0	0.0137	0.004
genus	Bacillus	Control	21	0.0136	0.009
genus	Lachnospiraceae NK3A20 group	Treated	8	0.0133	0.005
genus	Corynebacterium 1	Treated	28	0.0132	0.007
genus	Rikenellaceae RC9 gut group	Control	28	0.0132	0.010
genus	Bacteroides	Control	8	0.0130	0.014
genus	Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium	Control	21	0.0125	0.011
genus	Acinetobacter	Treated	8	0.0123	0.014
genus	Bacteroides	Treated	8	0.0121	0.005
genus	Lachnospiraceae NK3A20 group	Control	0	0.0121	0.003
genus	Corynebacterium 1	Control	28	0.0120	0.007
genus	Flavobacterium	Control	21	0.0120	0.012
genus	Lactobacillus	Treated	28	0.0120	0.008
genus	Christensenellaceae R-7 group	Control	21	0.0117	0.011
genus	Lachnospiraceae NK3A20 group	Treated	28	0.0117	0.007
genus	Acinetobacter	Treated	0	0.0116	0.004
genus	Bacillus	Treated	21	0.0116	0.005
genus	Bacillus	Treated	8	0.0113	0.007
genus	Lachnospiraceae NK3A20 group	Control	8	0.0113	0.006
genus	Rikenellaceae RC9 gut group	Control	21	0.0113	0.006
genus	Sphingomonas	Control	21	0.0113	0.008
genus	Corynebacterium 1	Control	0	0.0112	0.008
genus	[Eubacterium] coprostanoligenes group	Control	8	0.0111	0.011
genus	Acinetobacter	Control	8	0.0110	0.005
genus	Bacteroides	Treated	28	0.0106	0.007
genus	Shewanella	Control	28	0.0106	0.005
genus	Acinetobacter	Treated	28	0.0105	0.005
genus	Acinetobacter	Control	21	0.0104	0.005
genus	Clostridium sensu stricto 1	Treated	0	0.0104	0.006
genus	[Eubacterium] coprostanoligenes group	Control	21	0.0103	0.006
genus	Achromobacter	Control	28	0.0102	0.006
order	Clostridiales	Control	0	0.3586	0.158
order	Clostridiales	Treated	21	0.2907	0.161
order	Clostridiales	Treated	0	0.2875	0.092
order	Clostridiales	Control	8	0.2556	0.132
order	Clostridiales	Treated	28	0.2475	0.086
order	Clostridiales	Treated	8	0.2414	0.118
order	Pseudomonadales	Control	28	0.1931	0.065
order	Clostridiales	Control	21	0.1766	0.084
order	Clostridiales	Control	28	0.1437	0.102
order	Bacteroidales	Control	0	0.1207	0.024
order	Bacteroidales	Treated	21	0.1176	0.042
order	Pseudomonadales	Control	21	0.1169	0.051
order	Pseudomonadales	Treated	28	0.1128	0.075
order	Bacteroidales	Treated	0	0.1111	0.024
order	Pseudomonadales	Control	8	0.1074	0.067
order	Rhizobiales	Control	28	0.1032	0.054
order	Bacteroidales	Control	8	0.1028	0.024
order	Bacteroidales	Treated	28	0.0992	0.039
order	Bacteroidales	Treated	8	0.0977	0.034
order	Pseudomonadales	Treated	8	0.0956	0.063
order	Pseudomonadales	Treated	0	0.0948	0.031
order	Rhizobiales	Control	21	0.0853	0.041
order	Pseudomonadales	Control	0	0.0823	0.038
order	Propionibacteriales	Control	28	0.0811	0.029
order	Pseudomonadales	Treated	21	0.0773	0.051
order	Bacteroidales	Control	21	0.0700	0.018
order	Bacillales	Treated	8	0.0693	0.016
order	Bacteroidales	Control	28	0.0682	0.047
order	Bacillales	Control	8	0.0665	0.047
order	Rhizobiales	Treated	28	0.0619	0.048
order	Rhizobiales	Treated	8	0.0611	0.035
order	Rhizobiales	Control	8	0.0609	0.042
order	Lactobacillales	Treated	28	0.0604	0.018
order	Lactobacillales	Treated	0	0.0596	0.013
order	Lactobacillales	Control	8	0.0579	0.026
order	Micrococcales	Treated	8	0.0550	0.018
order	Propionibacteriales	Control	21	0.0550	0.018
order	Oceanospirillales	Control	28	0.0544	0.022
order	Lactobacillales	Treated	8	0.0534	0.017
order	Micrococcales	Control	21	0.0530	0.015
order	Micrococcales	Treated	0	0.0524	0.013
order	Micrococcales	Control	28	0.0519	0.022
order	Micrococcales	Treated	28	0.0506	0.017
order	Lactobacillales	Treated	21	0.0500	0.029
order	Propionibacteriales	Treated	28	0.0499	0.017
order	Bacillales	Control	21	0.0497	0.009
order	Bacillales	Control	28	0.0493	0.026
order	Lactobacillales	Control	0	0.0491	0.028
order	Rhizobiales	Treated	21	0.0484	0.030
order	Bacillales	Treated	28	0.0475	0.018
order	Bacillales	Treated	0	0.0465	0.014
order	Bacillales	Treated	21	0.0452	0.014
order	Propionibacteriales	Treated	0	0.0442	0.015
order	Propionibacteriales	Control	8	0.0431	0.020
order	Micrococcales	Control	8	0.0429	0.016
order	Propionibacteriales	Control	0	0.0427	0.028
order	Propionibacteriales	Treated	8	0.0409	0.019
order	Micrococcales	Treated	21	0.0401	0.022
order	Micrococcales	Control	0	0.0399	0.023
order	Rhizobiales	Control	0	0.0387	0.030
order	Rhizobiales	Treated	0	0.0384	0.029
order	Lactobacillales	Control	21	0.0380	0.018
order	Bacillales	Control	0	0.0374	0.017
order	Lactobacillales	Control	28	0.0363	0.025
order	Oceanospirillales	Control	21	0.0340	0.016
order	Oceanospirillales	Control	8	0.0331	0.024
order	Corynebacteriales	Control	21	0.0324	0.013
order	Oceanospirillales	Treated	28	0.0319	0.023
order	Propionibacteriales	Treated	21	0.0292	0.016
order	Corynebacteriales	Treated	8	0.0285	0.012
order	Betaproteobacteriales	Control	21	0.0279	0.013
order	Oceanospirillales	Treated	8	0.0278	0.020
order	Corynebacteriales	Treated	28	0.0270	0.008
order	Corynebacteriales	Control	28	0.0255	0.011
order	Sphingomonadales	Control	21	0.0253	0.012
order	Corynebacteriales	Control	8	0.0251	0.016
order	Alteromonadales	Control	28	0.0250	0.008
order	Corynebacteriales	Treated	0	0.0239	0.007
order	Oceanospirillales	Treated	0	0.0236	0.007
order	Oceanospirillales	Control	0	0.0225	0.010
order	Oceanospirillales	Treated	21	0.0225	0.016
order	Flavobacteriales	Control	21	0.0212	0.013
order	Alteromonadales	Treated	28	0.0209	0.006
order	Alteromonadales	Treated	0	0.0186	0.006
order	Sphingomonadales	Treated	8	0.0182	0.013
order	Corynebacteriales	Control	0	0.0176	0.011
order	Betaproteobacteriales	Control	28	0.0175	0.009
order	Alteromonadales	Control	8	0.0163	0.005
order	Corynebacteriales	Treated	21	0.0157	0.006
order	Betaproteobacteriales	Treated	21	0.0155	0.012
order	Sphingomonadales	Treated	21	0.0154	0.016
order	Alteromonadales	Control	0	0.0151	0.007
order	Alteromonadales	Treated	8	0.0151	0.008
order	Flavobacteriales	Treated	0	0.0151	0.002
order	Flavobacteriales	Treated	21	0.0149	0.015
order	Alteromonadales	Treated	21	0.0136	0.012
order	Aeromonadales	Treated	28	0.0131	0.004
order	Alteromonadales	Control	21	0.0129	0.006
order	Betaproteobacteriales	Control	8	0.0125	0.012
order	Betaproteobacteriales	Treated	8	0.0124	0.006
order	Sphingomonadales	Control	8	0.0121	0.006
order	Sphingomonadales	Control	28	0.0121	0.009
order	Flavobacteriales	Treated	28	0.0118	0.005
order	Sphingomonadales	Treated	0	0.0118	0.014
order	Xanthomonadales	Control	21	0.0118	0.005
order	Flavobacteriales	Control	0	0.0113	0.006
order	Flavobacteriales	Treated	8	0.0110	0.003
order	Aeromonadales	Treated	0	0.0109	0.004
order	Erysipelotrichales	Control	8	0.0104	0.004
order	Aeromonadales	Control	28	0.0103	0.004
order	Aeromonadales	Control	0	0.0102	0.006
order	Betaproteobacteriales	Treated	28	0.0101	0.009
phylum	Firmicutes	Control	0	0.4610	0.127
phylum	Proteobacteria	Control	28	0.4594	0.161
phylum	Firmicutes	Treated	0	0.4081	0.087
phylum	Firmicutes	Treated	21	0.4007	0.147
phylum	Firmicutes	Control	8	0.3945	0.129
phylum	Firmicutes	Treated	8	0.3781	0.123
phylum	Firmicutes	Treated	28	0.3689	0.108
phylum	Proteobacteria	Control	21	0.3559	0.111
phylum	Proteobacteria	Treated	28	0.3000	0.164
phylum	Proteobacteria	Control	8	0.2911	0.147
phylum	Proteobacteria	Treated	8	0.2855	0.147
phylum	Firmicutes	Control	21	0.2753	0.090
phylum	Proteobacteria	Treated	0	0.2507	0.079
phylum	Proteobacteria	Treated	21	0.2458	0.127
phylum	Firmicutes	Control	28	0.2414	0.119
phylum	Proteobacteria	Control	0	0.2176	0.104
phylum	Actinobacteria	Control	21	0.1785	0.029
phylum	Actinobacteria	Control	28	0.1785	0.045
phylum	Actinobacteria	Treated	8	0.1577	0.039
phylum	Actinobacteria	Treated	28	0.1540	0.021
phylum	Bacteroidetes	Treated	21	0.1487	0.025
phylum	Actinobacteria	Treated	0	0.1438	0.033
phylum	Actinobacteria	Control	8	0.1344	0.049
phylum	Bacteroidetes	Control	0	0.1341	0.023
phylum	Bacteroidetes	Treated	0	0.1308	0.021
phylum	Actinobacteria	Control	0	0.1225	0.059
phylum	Actinobacteria	Treated	21	0.1149	0.038
phylum	Bacteroidetes	Control	8	0.1148	0.026
phylum	Bacteroidetes	Treated	8	0.1147	0.035
phylum	Bacteroidetes	Treated	28	0.1135	0.044
phylum	Bacteroidetes	Control	21	0.1120	0.035
phylum	Bacteroidetes	Control	28	0.0766	0.050
phylum	Cyanobacteria	Treated	28	0.0146	0.003
phylum	Acidobacteria	Control	21	0.0142	0.009
phylum	Acidobacteria	Treated	21	0.0128	0.022
phylum	Cyanobacteria	Treated	0	0.0113	0.005
phylum	Planctomycetes	Treated	21	0.0103	0.018

##Class

Dclass <- D %>%
  filter(level=="class")

p <- ggplot(Dclass, aes(x=factor(1), y=avg_abund, fill=new_taxa)) + geom_bar(width=1,stat="identity", position = "fill")
p <- p + facet_grid(timepoint~treatment)
p <- p + guides(fill = guide_legend(title = "Class")) 
p <- p + geom_label_repel(aes(label = paste0(avg_abund*100, "%")), position=position_stack (vjust=0.5), size=4, show.legend = F)
my_palette = get_palette(c("green3","gold","blue","magenta","cyan","yellow","red","gray","purple", "darkorange1","pink1", "darkorchid1", "seagreen2"), length(unique(Dclass$new_taxa)))
p <- p + xlab("relative abundances") + ylab("percentages")
p <- p + scale_fill_manual(values = my_palette)
p <- p + theme(text = element_text(size=10),
               axis.text.x = element_text(size=8),
               # axis.text.y = element_text(size=4),
               strip.text = element_text(size = 8),
               axis.text.y = element_blank(),
               axis.ticks.y = element_blank(),
               legend.text=element_text(size=10),
               legend.title=element_text(size=10))
print(p)

#ggsave(p, height = 8, width = 8, filename ="taxonomy_class_bargraph_milk.png")

##Family

Dfamily <- D %>%
  filter(level=="family")

p <- ggplot(Dfamily, aes(x=factor(1), y=avg_abund, fill=new_taxa)) + geom_bar(width=1,stat="identity", position = "fill")
p <- p + facet_grid(timepoint~treatment)
p <- p + guides(fill = guide_legend(title = "Family")) 
#p <- p + geom_label_repel(aes(label = paste0(avg_abund*100, "%")), position=position_stack (vjust=0.5), size=4, show.legend = F)
my_palette2 = get_palette(c("green3","gold","blue","magenta","cyan","yellow","red","gray","purple","brown","black", "darkorange1","pink1", "darkorchid1", "seagreen2", "darkmagenta", "burlywood1", "maroon", "darkred", "burlywood3", "chartreuse4", "coral", "peachpuff", "mediumorchid3", "yellow3", "turquoise4", "snow", "slategray3", "orangered", "olivedrab", "plum", "lightcyan", "gray38", "forestgreen", "firebrick1"), length(unique(Dfamily$new_taxa)))
p <- p + xlab("relative abundances") + ylab("percentages")
p <- p + scale_fill_manual(values = my_palette2)
p <- p + theme(text = element_text(size=10),
               axis.text.x = element_text(size=8),
               # axis.text.y = element_text(size=4),
               strip.text = element_text(size = 8),
               axis.text.y = element_blank(),
               axis.ticks.y = element_blank(),
               legend.text=element_text(size=10),
               legend.title=element_text(size=10))
p

#ggsave(p, height = 8, width = 8, filename ="taxonomy_family_bargraph_MILK.png")

Genera

Dgenera <- D %>%
  filter(level=="genus")

p <- ggplot(Dgenera, aes(x=factor(1), y=avg_abund, fill=new_taxa)) + geom_bar(width=1,stat="identity", position = "fill")
p <- p + facet_grid(timepoint~treatment)
p <- p + guides(fill = guide_legend(title = "Genera")) 
my_palette2 = get_palette(c("green3","gold","blue","magenta","cyan","yellow","red","gray","purple","brown","black", "darkorange1","pink1", "darkorchid1", "seagreen2", "darkmagenta", "burlywood1", "maroon", "darkred", "burlywood3", "chartreuse4", "coral", "peachpuff", "mediumorchid3", "yellow3", "turquoise4", "snow", "slategray3", "orangered", "olivedrab", "plum", "lightcyan", "gray38", "forestgreen", "firebrick1"), length(unique(Dgenera$new_taxa)))
p <- p + xlab("relative abundances") + ylab("percentages")
p <- p + scale_fill_manual(values = my_palette2)
p <- p + theme(text = element_text(size=10),
               axis.text.x = element_text(size=8),
               # axis.text.y = element_text(size=4),
               strip.text = element_text(size = 8),
               axis.text.y = element_blank(),
               axis.ticks.y = element_blank(),
               legend.text=element_text(size=5),
               legend.title=element_text(size=5))
print(p)

#ggsave(p, height = 8, width = 8, filename ="taxonomy_genera_bargraph_MILK.png")

##Order

Dorder <- D %>%
  filter(level=="order")

p <- ggplot(Dorder, aes(x=factor(1), y=avg_abund, fill=new_taxa)) + geom_bar(width=1,stat="identity", position = "fill")
p <- p + facet_grid(timepoint~treatment)
p <- p + guides(fill = guide_legend(title = "Order")) 
my_palette2 = get_palette(c("red","darkred", "burlywood3", "chartreuse4","gray","gold","blue","magenta","cyan","purple","green3","yellow","brown","black", "darkorange1","pink1", "darkorchid1", "seagreen2", "darkmagenta", "burlywood1", "maroon",  "coral", "peachpuff", "mediumorchid3", "yellow3", "turquoise4", "snow", "slategray3", "orangered", "olivedrab", "plum", "lightcyan", "gray38", "forestgreen", "firebrick1"), length(unique(Dorder$new_taxa)))
p <- p + xlab("relative abundances") + ylab("percentages")
p <- p + scale_fill_manual(values = my_palette2)
p <- p + theme(text = element_text(size=10),
               axis.text.x = element_text(size=8),
               # axis.text.y = element_text(size=4),
               strip.text = element_text(size = 8),
               axis.text.y = element_blank(),
               axis.ticks.y = element_blank(),
               legend.text=element_text(size=10),
               legend.title=element_text(size=10))
print(p)

#ggsave(p, height = 8, width = 8, filename ="taxonomy_order_bargraph_MILK.png")

##Phylum

Dphylum <- D %>%
  filter(level=="phylum")

p <- ggplot(Dphylum, aes(x=factor(1), y=avg_abund, fill=new_taxa)) + geom_bar(width=1,stat="identity", position = "fill")
p <- p + facet_grid(timepoint~treatment)
p <- p + guides(fill = guide_legend(title = "Phylum")) 
p <- p + geom_label_repel(aes(label = paste0(avg_abund*100, "%")), position=position_stack (vjust=0.5), size=4, show.legend = F)
my_palette3 = get_palette(c("red", "green3","yellow","darkmagenta", "gray","lightcyan", "gold","blue"), length(unique(Dphylum$new_taxa)))
p <- p + xlab("relative abundances") + ylab("percentages")
p <- p + scale_fill_manual(values = my_palette3)
p <- p + theme(text = element_text(size=10),
               axis.text.x = element_text(size=8),
               # axis.text.y = element_text(size=4),
               strip.text = element_text(size = 8),
               axis.text.y = element_blank(),
               axis.ticks.y = element_blank(),
               legend.text=element_text(size=10),
               legend.title=element_text(size=10))
print(p)

#ggsave(p, height = 8, width = 8, filename ="taxonomy_phylum_bargraph_MILK.png")

Same results, but in wide-format (treatments on the horizontal axis): relative abundances (no standard deviations):

level	new_taxa	timepoint	Control	Treated
phylum	Acidobacteria	21	0.0142	0.0128
phylum	Actinobacteria	0	0.1225	0.1438
phylum	Actinobacteria	8	0.1344	0.1577
phylum	Actinobacteria	21	0.1785	0.1149
phylum	Actinobacteria	28	0.1785	0.1540
phylum	Bacteroidetes	0	0.1341	0.1308
phylum	Bacteroidetes	8	0.1148	0.1147
phylum	Bacteroidetes	21	0.1120	0.1487
phylum	Bacteroidetes	28	0.0766	0.1135
phylum	Cyanobacteria	0	NA	0.0113
phylum	Cyanobacteria	28	NA	0.0146
phylum	Firmicutes	0	0.4610	0.4081
phylum	Firmicutes	8	0.3945	0.3781
phylum	Firmicutes	21	0.2753	0.4007
phylum	Firmicutes	28	0.2414	0.3689
phylum	Planctomycetes	21	NA	0.0103
phylum	Proteobacteria	0	0.2176	0.2507
phylum	Proteobacteria	8	0.2911	0.2855
phylum	Proteobacteria	21	0.3559	0.2458
phylum	Proteobacteria	28	0.4594	0.3000
class	Actinobacteria	0	0.1109	0.1334
class	Actinobacteria	8	0.1237	0.1444
class	Actinobacteria	21	0.1590	0.1008
class	Actinobacteria	28	0.1734	0.1416
class	Alphaproteobacteria	0	0.0599	0.0649
class	Alphaproteobacteria	8	0.0915	0.0995
class	Alphaproteobacteria	21	0.1331	0.0810
class	Alphaproteobacteria	28	0.1358	0.0857
class	Bacilli	0	0.0864	0.1061
class	Bacilli	8	0.1244	0.1227
class	Bacilli	21	0.0877	0.0952
class	Bacilli	28	0.0856	0.1079
class	Bacteroidia	0	0.1341	0.1308
class	Bacteroidia	8	0.1148	0.1147
class	Bacteroidia	21	0.1120	0.1487
class	Bacteroidia	28	0.0766	0.1135
class	Clostridia	0	0.3587	0.2875
class	Clostridia	8	0.2556	0.2419
class	Clostridia	21	0.1766	0.2907
class	Clostridia	28	0.1438	0.2478
class	Erysipelotrichia	8	0.0104	NA
class	Gammaproteobacteria	0	0.1545	0.1826
class	Gammaproteobacteria	8	0.1972	0.1801
class	Gammaproteobacteria	21	0.2209	0.1602
class	Gammaproteobacteria	28	0.3224	0.2116
order	Aeromonadales	0	0.0102	0.0109
order	Aeromonadales	28	0.0103	0.0131
order	Alteromonadales	0	0.0151	0.0186
order	Alteromonadales	8	0.0163	0.0151
order	Alteromonadales	21	0.0129	0.0136
order	Alteromonadales	28	0.0250	0.0209
order	Bacillales	0	0.0374	0.0465
order	Bacillales	8	0.0665	0.0693
order	Bacillales	21	0.0497	0.0452
order	Bacillales	28	0.0493	0.0475
order	Bacteroidales	0	0.1207	0.1111
order	Bacteroidales	8	0.1028	0.0977
order	Bacteroidales	21	0.0700	0.1176
order	Bacteroidales	28	0.0682	0.0992
order	Betaproteobacteriales	8	0.0125	0.0124
order	Betaproteobacteriales	21	0.0279	0.0155
order	Betaproteobacteriales	28	0.0175	0.0101
order	Clostridiales	0	0.3586	0.2875
order	Clostridiales	8	0.2556	0.2414
order	Clostridiales	21	0.1766	0.2907
order	Clostridiales	28	0.1437	0.2475
order	Corynebacteriales	0	0.0176	0.0239
order	Corynebacteriales	8	0.0251	0.0285
order	Corynebacteriales	21	0.0324	0.0157
order	Corynebacteriales	28	0.0255	0.0270
order	Erysipelotrichales	8	0.0104	NA
order	Flavobacteriales	0	0.0113	0.0151
order	Flavobacteriales	8	NA	0.0110
order	Flavobacteriales	21	0.0212	0.0149
order	Flavobacteriales	28	NA	0.0118
order	Lactobacillales	0	0.0491	0.0596
order	Lactobacillales	8	0.0579	0.0534
order	Lactobacillales	21	0.0380	0.0500
order	Lactobacillales	28	0.0363	0.0604
order	Micrococcales	0	0.0399	0.0524
order	Micrococcales	8	0.0429	0.0550
order	Micrococcales	21	0.0530	0.0401
order	Micrococcales	28	0.0519	0.0506
order	Oceanospirillales	0	0.0225	0.0236
order	Oceanospirillales	8	0.0331	0.0278
order	Oceanospirillales	21	0.0340	0.0225
order	Oceanospirillales	28	0.0544	0.0319
order	Propionibacteriales	0	0.0427	0.0442
order	Propionibacteriales	8	0.0431	0.0409
order	Propionibacteriales	21	0.0550	0.0292
order	Propionibacteriales	28	0.0811	0.0499
order	Pseudomonadales	0	0.0823	0.0948
order	Pseudomonadales	8	0.1074	0.0956
order	Pseudomonadales	21	0.1169	0.0773
order	Pseudomonadales	28	0.1931	0.1128
order	Rhizobiales	0	0.0387	0.0384
order	Rhizobiales	8	0.0609	0.0611
order	Rhizobiales	21	0.0853	0.0484
order	Rhizobiales	28	0.1032	0.0619
order	Sphingomonadales	0	NA	0.0118
order	Sphingomonadales	8	0.0121	0.0182
order	Sphingomonadales	21	0.0253	0.0154
order	Sphingomonadales	28	0.0121	NA
order	Xanthomonadales	21	0.0118	NA
family	Bacillaceae	8	0.0104	0.0159
family	Bacillaceae	21	0.0151	0.0132
family	Bacteroidaceae	0	0.0205	0.0164
family	Bacteroidaceae	8	0.0130	0.0121
family	Bacteroidaceae	21	NA	0.0165
family	Bacteroidaceae	28	NA	0.0106
family	Beijerinckiaceae	0	0.0236	0.0246
family	Beijerinckiaceae	8	0.0459	0.0424
family	Beijerinckiaceae	21	0.0453	0.0252
family	Beijerinckiaceae	28	0.0675	0.0345
family	Burkholderiaceae	8	0.0118	0.0117
family	Burkholderiaceae	21	0.0230	0.0118
family	Burkholderiaceae	28	0.0165	NA
family	Carnobacteriaceae	0	0.0132	0.0178
family	Carnobacteriaceae	8	0.0131	0.0135
family	Carnobacteriaceae	21	NA	0.0132
family	Carnobacteriaceae	28	NA	0.0132
family	Christensenellaceae	0	0.0312	0.0261
family	Christensenellaceae	8	0.0229	0.0166
family	Christensenellaceae	21	0.0117	0.0242
family	Christensenellaceae	28	NA	0.0202
family	Clostridiaceae 1	0	NA	0.0119
family	Clostridiaceae 1	8	0.0103	NA
family	Corynebacteriaceae	0	0.0153	0.0194
family	Corynebacteriaceae	8	0.0207	0.0214
family	Corynebacteriaceae	21	0.0239	0.0106
family	Corynebacteriaceae	28	0.0201	0.0190
family	Erysipelotrichaceae	8	0.0104	NA
family	Family XIII	0	0.0130	0.0108
family	Flavobacteriaceae	0	NA	0.0109
family	Flavobacteriaceae	21	0.0156	0.0129
family	Halomonadaceae	0	0.0217	0.0226
family	Halomonadaceae	8	0.0324	0.0258
family	Halomonadaceae	21	0.0329	0.0216
family	Halomonadaceae	28	0.0514	0.0303
family	Lachnospiraceae	0	0.0734	0.0626
family	Lachnospiraceae	8	0.0598	0.0558
family	Lachnospiraceae	21	0.0423	0.0590
family	Lachnospiraceae	28	0.0317	0.0582
family	Lactobacillaceae	28	NA	0.0120
family	Microbacteriaceae	21	0.0124	NA
family	Micrococcaceae	0	0.0287	0.0348
family	Micrococcaceae	8	0.0287	0.0338
family	Micrococcaceae	21	0.0239	0.0235
family	Micrococcaceae	28	0.0348	0.0352
family	Moraxellaceae	0	0.0369	0.0441
family	Moraxellaceae	8	0.0405	0.0363
family	Moraxellaceae	21	0.0344	0.0275
family	Moraxellaceae	28	0.0522	0.0456
family	Nocardioidaceae	21	0.0154	NA
family	Peptostreptococcaceae	0	0.0146	0.0187
family	Peptostreptococcaceae	8	0.0159	0.0197
family	Peptostreptococcaceae	21	0.0168	0.0136
family	Peptostreptococcaceae	28	NA	0.0204
family	Prevotellaceae	0	0.0354	0.0371
family	Prevotellaceae	8	0.0364	0.0322
family	Prevotellaceae	21	0.0260	0.0427
family	Prevotellaceae	28	0.0272	0.0333
family	Propionibacteriaceae	0	0.0379	0.0389
family	Propionibacteriaceae	8	0.0379	0.0359
family	Propionibacteriaceae	21	0.0396	0.0234
family	Propionibacteriaceae	28	0.0759	0.0445
family	Pseudomonadaceae	0	0.0454	0.0507
family	Pseudomonadaceae	8	0.0668	0.0593
family	Pseudomonadaceae	21	0.0825	0.0497
family	Pseudomonadaceae	28	0.1409	0.0672
family	Rhizobiaceae	0	0.0105	NA
family	Rhizobiaceae	8	NA	0.0110
family	Rhizobiaceae	21	0.0248	0.0152
family	Rhizobiaceae	28	0.0268	0.0174
family	Rikenellaceae	0	0.0345	0.0329
family	Rikenellaceae	8	0.0256	0.0247
family	Rikenellaceae	21	0.0173	0.0322
family	Rikenellaceae	28	0.0188	0.0311
family	Ruminococcaceae	0	0.2013	0.1397
family	Ruminococcaceae	8	0.1210	0.1189
family	Ruminococcaceae	21	0.0813	0.1613
family	Ruminococcaceae	28	0.0757	0.1167
family	Shewanellaceae	28	0.0119	NA
family	Sphingomonadaceae	0	NA	0.0118
family	Sphingomonadaceae	8	0.0121	0.0182
family	Sphingomonadaceae	21	0.0253	0.0154
family	Sphingomonadaceae	28	0.0121	NA
family	Staphylococcaceae	0	0.0207	0.0224
family	Staphylococcaceae	8	0.0438	0.0411
family	Staphylococcaceae	21	0.0261	0.0228
family	Staphylococcaceae	28	0.0316	0.0273
family	Streptococcaceae	0	0.0256	0.0290
family	Streptococcaceae	8	0.0299	0.0244
family	Streptococcaceae	21	0.0161	0.0226
family	Streptococcaceae	28	0.0181	0.0296
family	Xanthobacteraceae	21	0.0118	NA
family	Xanthomonadaceae	21	0.0117	NA
genus	[Eubacterium] coprostanoligenes group	0	0.0219	0.0190
genus	[Eubacterium] coprostanoligenes group	8	0.0111	0.0169
genus	[Eubacterium] coprostanoligenes group	21	0.0103	0.0192
genus	[Eubacterium] coprostanoligenes group	28	NA	0.0185
genus	Achromobacter	28	0.0102	NA
genus	Acinetobacter	0	NA	0.0116
genus	Acinetobacter	8	0.0110	0.0123
genus	Acinetobacter	21	0.0104	NA
genus	Acinetobacter	28	0.0221	0.0105
genus	Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium	21	0.0125	NA
genus	Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium	28	0.0144	NA
genus	Bacillus	8	NA	0.0113
genus	Bacillus	21	0.0136	0.0116
genus	Bacteroides	0	0.0205	0.0164
genus	Bacteroides	8	0.0130	0.0121
genus	Bacteroides	21	NA	0.0165
genus	Bacteroides	28	NA	0.0106
genus	Christensenellaceae R-7 group	0	0.0308	0.0259
genus	Christensenellaceae R-7 group	8	0.0227	0.0166
genus	Christensenellaceae R-7 group	21	0.0117	0.0241
genus	Christensenellaceae R-7 group	28	NA	0.0202
genus	Clostridium sensu stricto 1	0	NA	0.0104
genus	Corynebacterium 1	0	0.0112	0.0139
genus	Corynebacterium 1	8	0.0154	0.0161
genus	Corynebacterium 1	21	0.0163	NA
genus	Corynebacterium 1	28	0.0120	0.0132
genus	Cutibacterium	0	0.0365	0.0360
genus	Cutibacterium	8	0.0350	0.0307
genus	Cutibacterium	21	0.0361	0.0209
genus	Cutibacterium	28	0.0734	0.0416
genus	Flavobacterium	21	0.0120	NA
genus	Halomonas	0	0.0211	0.0219
genus	Halomonas	8	0.0313	0.0251
genus	Halomonas	21	0.0320	0.0212
genus	Halomonas	28	0.0511	0.0298
genus	Lachnospiraceae NK3A20 group	0	0.0121	0.0137
genus	Lachnospiraceae NK3A20 group	8	0.0113	0.0133
genus	Lachnospiraceae NK3A20 group	28	NA	0.0117
genus	Lactobacillus	28	NA	0.0120
genus	Methylobacterium	0	0.0184	0.0194
genus	Methylobacterium	8	0.0394	0.0349
genus	Methylobacterium	21	0.0401	0.0219
genus	Methylobacterium	28	0.0603	0.0276
genus	Prevotella 1	0	0.0143	0.0157
genus	Prevotella 1	8	0.0196	0.0164
genus	Prevotella 1	21	0.0161	0.0217
genus	Prevotella 1	28	0.0197	0.0140
genus	Pseudomonas	0	0.0453	0.0504
genus	Pseudomonas	8	0.0666	0.0592
genus	Pseudomonas	21	0.0825	0.0495
genus	Pseudomonas	28	0.1405	0.0671
genus	Psychrobacter	0	0.0249	0.0292
genus	Psychrobacter	8	0.0271	0.0232
genus	Psychrobacter	21	0.0183	0.0203
genus	Psychrobacter	28	0.0233	0.0283
genus	Rikenellaceae RC9 gut group	0	0.0213	0.0207
genus	Rikenellaceae RC9 gut group	8	0.0174	0.0148
genus	Rikenellaceae RC9 gut group	21	0.0113	0.0219
genus	Rikenellaceae RC9 gut group	28	0.0132	0.0223
genus	Ruminococcaceae UCG-005	0	0.0393	0.0303
genus	Ruminococcaceae UCG-005	8	0.0286	0.0244
genus	Ruminococcaceae UCG-005	21	0.0187	0.0356
genus	Ruminococcaceae UCG-005	28	0.0176	0.0241
genus	Ruminococcaceae UCG-010	0	0.0459	0.0354
genus	Ruminococcaceae UCG-010	8	0.0295	0.0277
genus	Ruminococcaceae UCG-010	21	0.0169	0.0362
genus	Ruminococcaceae UCG-010	28	0.0177	0.0291
genus	Ruminococcaceae UCG-013	0	0.0218	NA
genus	Ruminococcaceae UCG-013	21	NA	0.0161
genus	Ruminococcaceae UCG-014	0	0.0138	NA
genus	Shewanella	28	0.0106	NA
genus	Sphingomonas	21	0.0113	NA
genus	Staphylococcus	0	0.0189	0.0190
genus	Staphylococcus	8	0.0384	0.0367
genus	Staphylococcus	21	0.0224	0.0194
genus	Staphylococcus	28	0.0272	0.0243
genus	Streptococcus	0	0.0254	0.0283
genus	Streptococcus	8	0.0298	0.0233
genus	Streptococcus	21	0.0157	0.0217
genus	Streptococcus	28	0.0176	0.0287

timepoint

level	new_taxa	treatment	0	8	21	28
phylum	Acidobacteria	Control	NA	NA	0.0142	NA
phylum	Acidobacteria	Treated	NA	NA	0.0128	NA
phylum	Actinobacteria	Control	0.1225	0.1344	0.1785	0.1785
phylum	Actinobacteria	Treated	0.1438	0.1577	0.1149	0.1540
phylum	Bacteroidetes	Control	0.1341	0.1148	0.1120	0.0766
phylum	Bacteroidetes	Treated	0.1308	0.1147	0.1487	0.1135
phylum	Cyanobacteria	Treated	0.0113	NA	NA	0.0146
phylum	Firmicutes	Control	0.4610	0.3945	0.2753	0.2414
phylum	Firmicutes	Treated	0.4081	0.3781	0.4007	0.3689
phylum	Planctomycetes	Treated	NA	NA	0.0103	NA
phylum	Proteobacteria	Control	0.2176	0.2911	0.3559	0.4594
phylum	Proteobacteria	Treated	0.2507	0.2855	0.2458	0.3000
class	Actinobacteria	Control	0.1109	0.1237	0.1590	0.1734
class	Actinobacteria	Treated	0.1334	0.1444	0.1008	0.1416
class	Alphaproteobacteria	Control	0.0599	0.0915	0.1331	0.1358
class	Alphaproteobacteria	Treated	0.0649	0.0995	0.0810	0.0857
class	Bacilli	Control	0.0864	0.1244	0.0877	0.0856
class	Bacilli	Treated	0.1061	0.1227	0.0952	0.1079
class	Bacteroidia	Control	0.1341	0.1148	0.1120	0.0766
class	Bacteroidia	Treated	0.1308	0.1147	0.1487	0.1135
class	Clostridia	Control	0.3587	0.2556	0.1766	0.1438
class	Clostridia	Treated	0.2875	0.2419	0.2907	0.2478
class	Erysipelotrichia	Control	NA	0.0104	NA	NA
class	Gammaproteobacteria	Control	0.1545	0.1972	0.2209	0.3224
class	Gammaproteobacteria	Treated	0.1826	0.1801	0.1602	0.2116
order	Aeromonadales	Control	0.0102	NA	NA	0.0103
order	Aeromonadales	Treated	0.0109	NA	NA	0.0131
order	Alteromonadales	Control	0.0151	0.0163	0.0129	0.0250
order	Alteromonadales	Treated	0.0186	0.0151	0.0136	0.0209
order	Bacillales	Control	0.0374	0.0665	0.0497	0.0493
order	Bacillales	Treated	0.0465	0.0693	0.0452	0.0475
order	Bacteroidales	Control	0.1207	0.1028	0.0700	0.0682
order	Bacteroidales	Treated	0.1111	0.0977	0.1176	0.0992
order	Betaproteobacteriales	Control	NA	0.0125	0.0279	0.0175
order	Betaproteobacteriales	Treated	NA	0.0124	0.0155	0.0101
order	Clostridiales	Control	0.3586	0.2556	0.1766	0.1437
order	Clostridiales	Treated	0.2875	0.2414	0.2907	0.2475
order	Corynebacteriales	Control	0.0176	0.0251	0.0324	0.0255
order	Corynebacteriales	Treated	0.0239	0.0285	0.0157	0.0270
order	Erysipelotrichales	Control	NA	0.0104	NA	NA
order	Flavobacteriales	Control	0.0113	NA	0.0212	NA
order	Flavobacteriales	Treated	0.0151	0.0110	0.0149	0.0118
order	Lactobacillales	Control	0.0491	0.0579	0.0380	0.0363
order	Lactobacillales	Treated	0.0596	0.0534	0.0500	0.0604
order	Micrococcales	Control	0.0399	0.0429	0.0530	0.0519
order	Micrococcales	Treated	0.0524	0.0550	0.0401	0.0506
order	Oceanospirillales	Control	0.0225	0.0331	0.0340	0.0544
order	Oceanospirillales	Treated	0.0236	0.0278	0.0225	0.0319
order	Propionibacteriales	Control	0.0427	0.0431	0.0550	0.0811
order	Propionibacteriales	Treated	0.0442	0.0409	0.0292	0.0499
order	Pseudomonadales	Control	0.0823	0.1074	0.1169	0.1931
order	Pseudomonadales	Treated	0.0948	0.0956	0.0773	0.1128
order	Rhizobiales	Control	0.0387	0.0609	0.0853	0.1032
order	Rhizobiales	Treated	0.0384	0.0611	0.0484	0.0619
order	Sphingomonadales	Control	NA	0.0121	0.0253	0.0121
order	Sphingomonadales	Treated	0.0118	0.0182	0.0154	NA
order	Xanthomonadales	Control	NA	NA	0.0118	NA
family	Bacillaceae	Control	NA	0.0104	0.0151	NA
family	Bacillaceae	Treated	NA	0.0159	0.0132	NA
family	Bacteroidaceae	Control	0.0205	0.0130	NA	NA
family	Bacteroidaceae	Treated	0.0164	0.0121	0.0165	0.0106
family	Beijerinckiaceae	Control	0.0236	0.0459	0.0453	0.0675
family	Beijerinckiaceae	Treated	0.0246	0.0424	0.0252	0.0345
family	Burkholderiaceae	Control	NA	0.0118	0.0230	0.0165
family	Burkholderiaceae	Treated	NA	0.0117	0.0118	NA
family	Carnobacteriaceae	Control	0.0132	0.0131	NA	NA
family	Carnobacteriaceae	Treated	0.0178	0.0135	0.0132	0.0132
family	Christensenellaceae	Control	0.0312	0.0229	0.0117	NA
family	Christensenellaceae	Treated	0.0261	0.0166	0.0242	0.0202
family	Clostridiaceae 1	Control	NA	0.0103	NA	NA
family	Clostridiaceae 1	Treated	0.0119	NA	NA	NA
family	Corynebacteriaceae	Control	0.0153	0.0207	0.0239	0.0201
family	Corynebacteriaceae	Treated	0.0194	0.0214	0.0106	0.0190
family	Erysipelotrichaceae	Control	NA	0.0104	NA	NA
family	Family XIII	Control	0.0130	NA	NA	NA
family	Family XIII	Treated	0.0108	NA	NA	NA
family	Flavobacteriaceae	Control	NA	NA	0.0156	NA
family	Flavobacteriaceae	Treated	0.0109	NA	0.0129	NA
family	Halomonadaceae	Control	0.0217	0.0324	0.0329	0.0514
family	Halomonadaceae	Treated	0.0226	0.0258	0.0216	0.0303
family	Lachnospiraceae	Control	0.0734	0.0598	0.0423	0.0317
family	Lachnospiraceae	Treated	0.0626	0.0558	0.0590	0.0582
family	Lactobacillaceae	Treated	NA	NA	NA	0.0120
family	Microbacteriaceae	Control	NA	NA	0.0124	NA
family	Micrococcaceae	Control	0.0287	0.0287	0.0239	0.0348
family	Micrococcaceae	Treated	0.0348	0.0338	0.0235	0.0352
family	Moraxellaceae	Control	0.0369	0.0405	0.0344	0.0522
family	Moraxellaceae	Treated	0.0441	0.0363	0.0275	0.0456
family	Nocardioidaceae	Control	NA	NA	0.0154	NA
family	Peptostreptococcaceae	Control	0.0146	0.0159	0.0168	NA
family	Peptostreptococcaceae	Treated	0.0187	0.0197	0.0136	0.0204
family	Prevotellaceae	Control	0.0354	0.0364	0.0260	0.0272
family	Prevotellaceae	Treated	0.0371	0.0322	0.0427	0.0333
family	Propionibacteriaceae	Control	0.0379	0.0379	0.0396	0.0759
family	Propionibacteriaceae	Treated	0.0389	0.0359	0.0234	0.0445
family	Pseudomonadaceae	Control	0.0454	0.0668	0.0825	0.1409
family	Pseudomonadaceae	Treated	0.0507	0.0593	0.0497	0.0672
family	Rhizobiaceae	Control	0.0105	NA	0.0248	0.0268
family	Rhizobiaceae	Treated	NA	0.0110	0.0152	0.0174
family	Rikenellaceae	Control	0.0345	0.0256	0.0173	0.0188
family	Rikenellaceae	Treated	0.0329	0.0247	0.0322	0.0311
family	Ruminococcaceae	Control	0.2013	0.1210	0.0813	0.0757
family	Ruminococcaceae	Treated	0.1397	0.1189	0.1613	0.1167
family	Shewanellaceae	Control	NA	NA	NA	0.0119
family	Sphingomonadaceae	Control	NA	0.0121	0.0253	0.0121
family	Sphingomonadaceae	Treated	0.0118	0.0182	0.0154	NA
family	Staphylococcaceae	Control	0.0207	0.0438	0.0261	0.0316
family	Staphylococcaceae	Treated	0.0224	0.0411	0.0228	0.0273
family	Streptococcaceae	Control	0.0256	0.0299	0.0161	0.0181
family	Streptococcaceae	Treated	0.0290	0.0244	0.0226	0.0296
family	Xanthobacteraceae	Control	NA	NA	0.0118	NA
family	Xanthomonadaceae	Control	NA	NA	0.0117	NA
genus	[Eubacterium] coprostanoligenes group	Control	0.0219	0.0111	0.0103	NA
genus	[Eubacterium] coprostanoligenes group	Treated	0.0190	0.0169	0.0192	0.0185
genus	Achromobacter	Control	NA	NA	NA	0.0102
genus	Acinetobacter	Control	NA	0.0110	0.0104	0.0221
genus	Acinetobacter	Treated	0.0116	0.0123	NA	0.0105
genus	Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium	Control	NA	NA	0.0125	0.0144
genus	Bacillus	Control	NA	NA	0.0136	NA
genus	Bacillus	Treated	NA	0.0113	0.0116	NA
genus	Bacteroides	Control	0.0205	0.0130	NA	NA
genus	Bacteroides	Treated	0.0164	0.0121	0.0165	0.0106
genus	Christensenellaceae R-7 group	Control	0.0308	0.0227	0.0117	NA
genus	Christensenellaceae R-7 group	Treated	0.0259	0.0166	0.0241	0.0202
genus	Clostridium sensu stricto 1	Treated	0.0104	NA	NA	NA
genus	Corynebacterium 1	Control	0.0112	0.0154	0.0163	0.0120
genus	Corynebacterium 1	Treated	0.0139	0.0161	NA	0.0132
genus	Cutibacterium	Control	0.0365	0.0350	0.0361	0.0734
genus	Cutibacterium	Treated	0.0360	0.0307	0.0209	0.0416
genus	Flavobacterium	Control	NA	NA	0.0120	NA
genus	Halomonas	Control	0.0211	0.0313	0.0320	0.0511
genus	Halomonas	Treated	0.0219	0.0251	0.0212	0.0298
genus	Lachnospiraceae NK3A20 group	Control	0.0121	0.0113	NA	NA
genus	Lachnospiraceae NK3A20 group	Treated	0.0137	0.0133	NA	0.0117
genus	Lactobacillus	Treated	NA	NA	NA	0.0120
genus	Methylobacterium	Control	0.0184	0.0394	0.0401	0.0603
genus	Methylobacterium	Treated	0.0194	0.0349	0.0219	0.0276
genus	Prevotella 1	Control	0.0143	0.0196	0.0161	0.0197
genus	Prevotella 1	Treated	0.0157	0.0164	0.0217	0.0140
genus	Pseudomonas	Control	0.0453	0.0666	0.0825	0.1405
genus	Pseudomonas	Treated	0.0504	0.0592	0.0495	0.0671
genus	Psychrobacter	Control	0.0249	0.0271	0.0183	0.0233
genus	Psychrobacter	Treated	0.0292	0.0232	0.0203	0.0283
genus	Rikenellaceae RC9 gut group	Control	0.0213	0.0174	0.0113	0.0132
genus	Rikenellaceae RC9 gut group	Treated	0.0207	0.0148	0.0219	0.0223
genus	Ruminococcaceae UCG-005	Control	0.0393	0.0286	0.0187	0.0176
genus	Ruminococcaceae UCG-005	Treated	0.0303	0.0244	0.0356	0.0241
genus	Ruminococcaceae UCG-010	Control	0.0459	0.0295	0.0169	0.0177
genus	Ruminococcaceae UCG-010	Treated	0.0354	0.0277	0.0362	0.0291
genus	Ruminococcaceae UCG-013	Control	0.0218	NA	NA	NA
genus	Ruminococcaceae UCG-013	Treated	NA	NA	0.0161	NA
genus	Ruminococcaceae UCG-014	Control	0.0138	NA	NA	NA
genus	Shewanella	Control	NA	NA	NA	0.0106
genus	Sphingomonas	Control	NA	NA	0.0113	NA
genus	Staphylococcus	Control	0.0189	0.0384	0.0224	0.0272
genus	Staphylococcus	Treated	0.0190	0.0367	0.0194	0.0243
genus	Streptococcus	Control	0.0254	0.0298	0.0157	0.0176
genus	Streptococcus	Treated	0.0283	0.0233	0.0217	0.0287

Finally,a bubble chart to visualize relative abundances per taxa and treatment:

## `summarise()` has grouped output by 'level', 'new_taxa'. You can override using the `.groups` argument.

Significance of treatments (+ timepoint)

The significance of differences between treatments (Control vs Treated with Essential Oil) was evaluated using a linear model (ANOVA) that included the effect of timepoints:

\[ counts_{ikj} = \mu + timepoint_k + treatment_j + e_{ikj} \]

This way, the variability due to region is removed when assessing the effect of treatments.

Significance of treatments (per timepoint)

The significance of differences between treatments (Control vs Treated with Essential Oil) was evaluated using a linear model (ANOVA) that included the effect of timepoints:

\[ counts_{ij} = \mu + treatment_j + e_{ij} \]

this way, the variability due to region is removed when assessing the effect of treatments.

## `summarise()` has grouped output by 'level', 'new_taxa', 'timepoint'. You can override using the `.groups` argument.

## # A tibble: 5 × 2
##   level    tot
##   <chr>  <dbl>
## 1 class   4.00
## 2 family  3.89
## 3 genus   3.60
## 4 order   3.99
## 5 phylum  4

# dd_counts$type <- c("ileum","rumen")[match(dd_counts$type,unique(dd_counts$type))]
# dd <- bind_rows(dd_rumen, dd_ileal)
# dd <- dd_counts %>% inner_join(dd, by = c("level" = "level", "new_taxa" = "new_taxa", "type" = "type"))
# dd %>% fwrite("significant_otus_relabund.csv", sep=",")

DX <- D %>%
  filter(`p.value` <= 0.05) %>%
  select(c(level,new_taxa,timepoint,`p.value`)) %>%
  arrange(level,`p.value`)

D0 <- mO %>%
  dplyr::group_by(level,new_taxa,timepoint,treatment) %>%
  dplyr::summarise(avg_counts = mean(counts))

## `summarise()` has grouped output by 'level', 'new_taxa', 'timepoint'. You can override using the `.groups` argument.

to_save = list(D,DX,D0)
save(to_save, file = "taxonomy_timepoint.RData")

load("taxonomy_timepoint.RData")
D <- to_save[[1]]
DX <- to_save[[2]]
D0 <- to_save[[3]]

dd <- spread(D0, key = treatment, value = avg_counts)
temp <- inner_join(DX,dd, by = c("level" = "level", "new_taxa" = "new_taxa", "timepoint" = "timepoint"))
fwrite(temp, file = "significant_otus.csv", col.names = TRUE, sep = ",")
print (dd)

## # A tibble: 5,472 × 5
## # Groups:   level, new_taxa, timepoint [5,472]
##    level new_taxa       timepoint Control Treated
##    <chr> <chr>          <fct>       <dbl>   <dbl>
##  1 class Acidimicrobiia 0           7.72    7.26 
##  2 class Acidimicrobiia 8           5.78    7.18 
##  3 class Acidimicrobiia 21         17.2    14.6  
##  4 class Acidimicrobiia 28          4.31    7.17 
##  5 class Acidobacteriia 0           0.145   0.175
##  6 class Acidobacteriia 8           2.41    4.64 
##  7 class Acidobacteriia 21          7.88    4.46 
##  8 class Acidobacteriia 28          2.41    0.302
##  9 class Actinobacteria 0         293.    379.   
## 10 class Actinobacteria 8         276.    335.   
## # … with 5,462 more rows

load("taxonomy_timepoint.RData")
D <- to_save[[1]]
DX <- to_save[[2]]
D0 <- to_save[[3]]

D0 <- mutate(D0, avg_counts = avg_counts+1) %>% spread(key = treatment, value = avg_counts)

D1 <- DX %>%
  inner_join(D0, by = c("level" = "level", "new_taxa" = "new_taxa", "timepoint" = "timepoint")) %>%
  mutate(p.value = -log10(p.value), Control = ifelse(log(Control) < 0,0,log10(Control)), Treated = ifelse(log(Treated) < 0, 0, log10(Treated))) %>%
  gather(key = "treatment", value = "counts", -c(level,new_taxa,timepoint,p.value))

D1$level <- factor(D1$level, levels = c("phylum","class","order","family","genus"))

p <- ggplot(D1, aes(x = treatment, y = new_taxa, group=level))
p <- p + geom_tile(aes(fill = counts), colour = "white")
p <- p + facet_grid(level~timepoint, space="free", scales = "free_y")
p <- p + scale_fill_gradient(low = "orange", high = "blue")
p <- p + theme(strip.text.y = element_text(size = 5), 
               strip.text.x = element_text(size = 6),
               # axis.text.y = element_text(size = 4),
               axis.text.x = element_text(size = 6),
               axis.title = element_text(size = 6))
p <- p + guides(fill=FALSE) + theme(axis.title.y = element_blank(),
                                    axis.text.y = element_blank(),
                                    axis.ticks.y = element_blank())

## Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> =
## "none")` instead.

# p
dd <- filter(D1, treatment == "Control") %>% mutate(variable = "p-value")

q <- ggplot(dd, aes(x = factor(1), y = new_taxa, group=level))
q <- q + geom_tile(aes(fill = p.value), colour = "white")
q <- q + facet_grid(level~variable, space="free", scales = "free_y")
q <- q + scale_fill_gradient(low = "orange", high = "blue")
q <- q + theme(strip.text = element_text(size = 4), 
               strip.text.x = element_text(size = 6),
               axis.text.y = element_text(size = 5),
               axis.title = element_text(size = 6))
q <- q + guides(fill=FALSE) + theme(
  # axis.title.x = element_blank(),
  # axis.text.x=element_blank(),
  # axis.ticks.x=element_blank(),
  strip.text.y = element_blank(),
  # axis.text.x = element_blank()
  axis.text.x = element_text(size = 6)
)

## Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> =
## "none")` instead.

q <- q + xlab("") 

figure_final <- ggarrange(q, p, widths=c(0.25, 0.75), 
                          labels=c("A", "B"))

print(figure_final)

#ggsave(filename = "heatmap_MILK.png", plot = figure_final, device = "png", width = 8, height = 10)